The present invention relates generally to novel cloning methods, to the DNA sequences obtained using these methods, the corresponding expression products of the DNA sequences and antibodies thereto, as well as to novel screening methods for compounds affecting protein activity. More specifically, the present invention provides novel complementation screening methods particularly useful in the isolation of DNAs encoding cyclic nucleotide phosphodiesterase polypeptides (PDEs) and RAS-related proteins. These DNAs, in turn, provide valuable materials useful as hybridization probes for related DNAs and useful in obtaining polypeptide expression products when used to transform suitable host cells.
Of interest to the present invention are the following discussions relating to the cyclic nucleotide phosphodiesterases and RAS-related proteins.
The RAS genes were first discovered as the transforming principles of the Harvey and Kirsten murine sarcoma viruses [Ellis et al., Nature, 292:506 (1981)]. The cellular homologs of the oncogenes of Harvey and Kirsten murine sarcoma viruses (H-RAS and K-RAS) constitute two members of the RAS gene family [Shimizu et al., Proc. Natl. Acad. Sci., 80:2112 (1983)]. A third member is N-RAS [Shimizu et al., Proc. Natl. Acad. Sci., 80:2112 (1983)]. These genes are known as oncogenes since point mutations in RAS can result in genes capable of transforming non-cancerous cells into cancerous cells [Tabin et al., Nature, 300:143 (1982); Reddy et al., Nature, 300:149 (1982); Taparowsky et al., Nature, 300:762 (1982)]. Many tumor cells contain RAS genes with such mutations [Capon et al., Nature, 302:33 (1983); Capon et al., Nature, 304:507 (1983); Shimizu et al., Nature, 304:497 (1983); Taparowsky et al., Cell, 34:581 (1983); Taparowsky et al., Nature, 300:762 (1982); Barbacid, Ann. Rev. Biochem., 56:779 (1987)]. Kitayana et al., Cell 56:77 (1989), described another "ras-related" gene called "K-rev" which showed revertant inducing activity of Kirsten-sarcoma virus transformed cells.
Despite the importance of the RAS oncogenes to our understanding of cancer, a complete understanding of the function of RAS genes in mammals has not yet been achieved. The RAS proteins are small proteins (21,000 daltons in mammals) which bind GTP and GDP [Papageorge et al., J. Virol., 44:509 (1982)]. The RAS proteins hydrolyze GTP slowly; specific cellular proteins can accelerate this process [McGrath et al., Nature, 310:644 (1984); Trahey et al., Science, 238:542 (1987)]. RAS proteins bind to the inner surface of the plasma membrane [Willingham et al., Cell, 19:1005 (1980)] and undergo a complex covalent modification at their carboxy termini [Hancock et al., Cell, 57:1167 (1989)]. The crystal structure of H-RAS is known (De Vos et al., Science, 239:888 (1988)].
The yeast Saccharomyces cerevisiae contains two genes, RAS1 and RAS2, that have structural and functional homology with mammalian RAS oncogenes [Powers et al., Cell, 36:607 (1984); Kataoka et al., Cell, 40:19 (1985); Defeo-Jones et al., Science, 228:179 (1985); Dhar et al., Nucl. Acids Res., 12:3611 (1984)]. Both RAS1 and RAS2 have been cloned from yeast plasmid libraries and the complete nucleotide sequence of their coding regions has been determined [Powers et al., Cell, 36:607 (1984); DeFeo-Jones et al., Nature, 306:707 (1983)]. The two genes encode proteins with nearly 90% identity to the first 80 amino acid positions of the mammalian RAS proteins, and nearly 50% identity to the next 80 amino acid positions. Yeast RAS1 and RAS2 proteins are more homologous to each other, with about 90% identity for the first 180 positions. After this, at nearly the same position that the mammalian RAS proteins begin to diverge from each other, the two yeast RAS proteins diverge radically. The yeast RAS proteins, like proteins encoded by the mammalian genes, terminate with the sequence cysAAX, where A is an aliphatic amino acid, and X is the terminal amino acid [Barbacid, Ann Rev. Biochem., 56:779 (1987)]. Monoclonal antibody directed against mammalian RAS proteins immunoprecipitates RAS proteins in yeast cells [Powers et al., Cell, 47:413 (1986)]. Thus, the yeast RAS proteins have the same overall structure and interrelationship as is found in the family of mammalian RAS proteins.
RAS genes have been detected in a wide variety of eukaryotic species, including Schizosaccharomyces pombe, Dictyostelium discoidiem and Drosophila melanogaster [Fukui et al., EMBO, 4:687 (1985); Reymond et al., Cell; 39:141 (1984); Shilo et al., Proc. Natl. Acad. Sci. (USA), 78:6789 (1981); Neuman-Silberberg, Cell, 37:1027 (1984)]. The widespread distribution of RAS genes in evolution indicates that studies of RAS in simple eukaryotic organisms may elucidate the normal cellular functions of RAS in mammals.
Extensive genetic analyses of the RAS1 and RAS2 of S. cerevisiae have been performed. By constructing in vitro RAS genes disrupted by selectable biochemical markers and introducing these by gene replacement into the RAS chromosomal loci, it has been determined that neither RAS1 nor RAS2 is, by itself, an essential gene. However, doubly RAS deficient (ras1.sup.- ras2.sup.-) spores of doubly heterozygous diploids are incapable of resuming vegetative growth. At least some RAS function is therefore required for viability of S. cerevisiae [Kataoka et al., Cell, 37:437 (1984)]. It has also been determined that RAS1 is located on chromosome XV, 7 centimorgans (cM) from ADE2 and 63 cM from HIS3: and that RAS2 is located on chromosome XIV, 2 cM from MET4 [Kataoka et al., Cell, 37:437 (1984)].
Mammalian RAS expressed in yeast can function to correct the phenotypic defects than otherwise would result from the loss of both RAS1 and RAS2 [Kataoka et al., Cell, 40:19 (1985)]. Conversely, yeast RAS1 is capable of functioning in vertebrate cells [De Feo-Jones et al., Science, 228:179 (1985)]. Thus, there has been sufficient conservation of structure between yeast and human RAS proteins to allow each to function in heterologous host cells.
The missense mutant, RAS2.sup.va119, which encodes valine in place of glycine at the nineteenth amino acid position, has the same sort of mutation that is found in some oncogenic mutants of mammalian RAS genes [Tabin et al., Nature, 300:143 (1982); Reddy et. al., Nature, 300:149 (1982); Taparowsky et al., Nature, 300:762 (1982)]. Diploid yeast cells that contain this mutation are incapable of sporulating efficiently, even when they contain wild-type RAS alleles [Kataoka et al., Cell, 37:437 (1984)]. When an activated form of the RAS2 gene (e.g., RAS2.sup.va119) is present in haploid cells, yeast cells fail to synthesize glycogen, are unable to arrest in G1, die rapidly upon nutrient starvation, and are acutely sensitive to heat shock [Toda et al., Cell, 40:27 (1985); Sass et al., Proc. Natl. Acad. Sci., 83:9303 (1986)].
S. cerevisiae strains containing RAS2.sup.va119 have growth and biochemical properties strikingly similar to yeast carrying the IAC or bcyl mutations, which activate the cyclic AMP (cAMP) pathway in yeast [Uno et al., J. Biol. Chem., 257:14110 (1981)]. Yeast strains carrying the IAC mutation have elevated levels of adenylyl cyclase activity which is responsible for catalyzing the conversion of ATP to cyclic-AMP. bcyl.sup.- cells lack the regulatory component of the cAMP dependent protein kinase [Uno et al., J. Biol. Chem., 257:14110 (1982); Toda et al., Mol. Cell. Biol., 7:1371 (1987)]. Yeast strains deficient in RAS function exhibit properties similar to adenylyl cyclase-deficient yeast [Toda et al., Cell, 40:27 (1985)]. The bcyl.sup.- mutation suppresses lethality in ras1.sup.- ras2.sup.- yeast. These results suggest that in the yeast S. cerevisiae, RAS proteins function in the cAMP signalling pathway.
Adenylyl cyclase has been shown to be controlled by RAS proteins [Toda et al., Cell, 40:27 (1985)]. RAS proteins, either from yeast or humans, can stimulate adenylyl cyclase up to fifty fold in in vitro biochemical assays. RAS proteins will stimulate adenylyl cyclase only when bound with GTP [Field et al., Mol. Cell. Biol., 8:2159 (1988)]. The phenotypes resulting from the activation of RAS, including sensitivity to heat shock and starvation, are primarily the result of overexpression or uncontrolled activation of the cAMP effector pathway via adenylyl cyclase [Kataoka et al., Cell, 37:437 (1984); Kataoka et al., Cell, 43:493 (1985); Toda et al., Cell, 40:27 (1985); Field et al., Mol. Cell. Biol., 8:2159 (1988)].
Cellular concentrations of cAMP are controlled not only by the rate of cAMP production by adenylyl cyclase but also by the rate of cAMP degradation by phosphodiesterases (PDEs). PDEs are the enzymes responsible for the degradation of cAMP to AMP and cGMP to GMP.
Two S. cerevisiae yeast genes, PDE1 and PDE2, which encode the low and high affinity cAMP phosphodiesterases, respectively, have been isolated [Sass et al., Proc. Natl. Acad. Sci., 83:9303 (1986); Nikawa et al., Mol. Cell. Biol., 7:3629 (1987)]. These genes were cloned from yeast genomic libraries by their ability to suppress the heat shock sensitivity in yeast cells harboring an activated RAS2.sup.va119 gene. Cells lacking the PDE genes (i.e., pde1.sup.- pde2.sup.- yeast) are heat shock sensitive, are deficient in glycogen accumulation, fail to grow on an acetate carbon source, and in general have defects due to activation of the cAMP signaling pathway [Nikawa et al., Mol. Cell. Biol., 7:3629 (1987)].
Genetic analysis clearly indicates that RAS proteins have other functions in S. cerevisiae in addition to stimulating adenylyl cyclase [Toda et al., Japan Sci. Soc. Press., Tokyo/VNU Sci. Press, pp. 253 (1987); Wigler et al., Cold Spring Harbor Symposium, LIII:649 (1988); Michaeli et al., EMBO, 8:3039 (1989)]. The precise biochemical nature of these functions is unknown. Experiments with other systems, such as S. pombe and Xenopus laevis oocytes, indicate that RAS stimulation of adenylyl cyclase is not widespread in evolution [Birchmeier et al., Cell, 43:615 (1985)]. It is unlikely that RAS stimulates adenylyl cyclase in mammals (Beckner et al., Nature, 317:1 (1985)).
While the cAMP effector pathway plays a role in heat shock and starvation in yeast, it plays other roles in higher organisms. For example, in mammals, cAMP is a "second messenger" that mediates the response of cells to a variety of hormones and neurotransmitters including calcitonin, chorionic gonadotropin, corticotropin, epinephrine, follicle-stimulating hormone, glucagon, luteinizing hormone, lipotropin, melanocyte-stimulating hormone, norepinephrine, parathyroid hormone, thyroid-stimulating hormone, and vasopressin.
In humans, cAMP has been implicated in a number of important physiological responses including smooth muscle relaxation, strength of cardiac contractility, release of histamine and other immunoreactive molecules, lymphocyte proliferation, and platelet aggregation [Robison et al., Cyclic AMP, Academic Press, New York and London (1971)].
Among its many functions cAMP has also been implicated in central nervous system function in both invertebrates and mammals. In particular, cAMP has been shown to play a role in learning and memory. For example, in Aplysia, the long term potentiation of neurons in the gill retraction reflex that occurs with learning is associated with alterations in activity of several components of the cAMP signaling pathway, particularly adenylyl cyclase and a cAMP dependent protein kinase [Schacher et al., Cold Spring Harbor Symp. Quant. Biol. LV:187-202 (1990)].
In Drosophila melanogaster numerous learning associated genes have been isolated, mutations in which affect learning. One of these genes is the dunce gene (dnc) which codes a cAMP specific phosphodiesterase (PDE). [Dudai, Y., Ann. Rev. Neurosci, 11:537-563 (1988); Qie, et al., J. Mol. Biol., 222:553-565 (1991)]. Electrophysiologic studies of neurons from dnc Drosophila have shown alterations in neuronal latency suggesting that the functional changes occurring in learning in wild-type flies may be similar to those seen in Aplysia [Zong, et al., Science, 251:198-201 (1991)].
Evidence for a functional role of dunce-like PDEs in the mammalian CNS comes from the use of cAMP specific PDE inhibitors, including the drug Rolipram which in addition to their ability to inhibit PDEs, have clinical activity as antidepressants [Eckmann, et al., Curr. Therapeutic Res., 43:291-295 (1988)].
In rat at least 4 different genes encoding dnc homologs have been identified. However, only 2 cDNAs encoding a human dnc homolog have been cloned and expressed. Livi, et al., (Mol. Cell Biol., 10:2678-2686 (1990)) have cloned and expressed a cDNA for a human, low K.sub.m, Rolipram sensitive cAMP phosphodiesterase. McLaughlin, et al., J. Biol. Chem., 265:6470-6476 (1993) have isolated a different cDNA encoding a low K.sub.m Rolipram sensitive cAMP phosphodiesterase.
Given the importance of cAMP in the regulation of a variety of metabolic and physiologic processes, considerable effort has been directed toward developing and evaluating cAMP analogues, as well as inhibitors of phosphodiesterases which may serve as pharmaceutical agents capable of altering cAMP levels which are associated with a variety of pathological conditions. As described above, one way to modulate cAMP levels in cells is through the modulation of cAMP phosphodiesterase activity. Certain drugs useful in treating heart failure, asthma, depression, and thrombosis, appear to work by inhibiting cAMP phosphodiesterases. However, the pharmaceutical industry has not been notably successful in finding suitably specific drugs which inhibit cAMP phosphodiesterases, in part because effective drug screens have not been available. In addition, most tissues contain so many different isoforms of phosphodiesterases that drug screening based on traditional methods involving inhibition of crude tissue extracts is unlikely to yield anything other than a broadly acting inhibitor of phosphodiesterases. Broadly acting inhibitors of cAMP phosphodiesterases, such as theophylline, have many deleterious side effects.
As noted above, PDE inhibitor research has as its goal the development of highly specific PDE inhibitors. This lack of PDE inhibitor specificity is in part attributable to the existence of several distinct molecular forms of PDE present within a single tissue type, indeed, present among the various cell types comprising a particular tissue type. These various forms can be distinguished according to substrate specificity (cAMP vs. cGMP), intracellular location (soluble vs. membrane bound), response to calmodulin and can, in certain instances, be selectively inhibited by various therapeutic agents. Developing agents that will selectively act upon PDEs is directed toward reproducing the desirable effects of cyclic nucleotides, e.g., bronchodilation, increased myocardial contractility, anti-inflammation, yet without causing the undesirable effects, e.g., increased heart rate or enhanced lipolysis.
One approach to screening agents for their potential utility as PDE inhibitors, e.g. drug screening, requires "kinetically pure" preparations of PDE enzymes. That is, the use of whole tissue homogenates or extracts is unlikely to identify inhibitors selective for an individual PDE isozyme because, as described above, most tissues are heterogeneous with respect to cell type and may contain multiple PDE isozymes.
At least five different families of PDEs have been described based on characteristics such as substrate specificity, kinetic properties, cellular regulatory control, size, and in some instances, modulation by selective inhibitors. [Beavo, Adv. in Second Mess. and Prot. Phosph. Res. 22:1-38 (1988)]. The five families include:
______________________________________ I Ca.sup.2+ /calmodulin-stimulated II cGMP-stimulated III cGMP-inhibited IV cAMP-specific V cGMP-specific ______________________________________
Within each family there are multiple forms of closely related PDEs. See Beavo, "Multiple Phosphodiesterase Isozymes Background, Nomenclature and Implications", pp. 3-15 In:Cyclic Nucleotide Phosphodiesterases: Structure, Regulation and Drug Action, Beavo, J. and Houslay, M. D., Eds.; John Wiley & Sons, New York (1990). See, also, Beavo, TIPS, 11:150 (1990).
Of the many distinct PDE enzymes now recognized, for only certain of the cGMP specific PDEs is complete cDNA sequence information available. With the acquisition of complete structural information for all PDEs, it may be possible to identify and localize (cellular and subcellular distribution) each PDE isozyme and thereby design isozyme-selective PDE inhibitors as therapeutic agents for specific diseases thereby minimizing untoward side-effects. However, the heterogeneity, instability, and relatively low abundance of some of the PDE isozymes have presented major obstacles in purifying and characterizing these enzymes. Thus, it is clear that the cloning and characterization of genes coding for PDEs will facilitate the design of more specific and more effective PDE inhibitors.
Several methods are presently available for cloning mammalian genes. A standard approach to cloning mammalian genes requires obtaining purified protein, determining a partial amino acid sequence of the purified protein, using the partial amino acid sequence to produce degenerate oligonucleotide probes, and screening cDNA libraries with these probes to obtain cDNA encoding the protein. This method is time consuming and, because of the degeneracy of the probes used, may identify sequences other than those encoding the protein(s) of interest. Many mammalian genes have been cloned this way including, for example, the gene encoding the cGMP phosphodiesterase expressed in retina [Ovchinnikov et al., FEBS, 223:169 (1987)].
A second approach to cloning genes encoding a protein of interest is to use a known gene as a probe to find homologs. This approach is particularly useful when members of a gene family or families are sufficiently homologous. The Drosophila melanogaster dunce phosphodiesterase gene was used, for example to clone rat homologs. Davis et al., Proc. Natl. Acad. Sci. (USA), 86:3604 (1989); and Swinnen et al., Proc. Natl.,Acad. Sci. (USA), 86:5325 (1989). Although additional members of one family of phosphodiesterase genes might be cloned once a first member of that family has been cloned, it is never known in advance whether the nucleotide sequences of genes belonging to different phosphodiesterase gene families will exhibit sufficient homology to use probes derived from one family to identify members of another family.
Yet another approach to cloning genes is known as complementation. A number of researchers have reported the isolation of yeast genes by their ability to complement a mutation/defect in the corresponding gene in another yeast. See, for example: McKnight et al., EMBO J., 4:2093 (1985)--Aspergillus nidulans gene encoding alcohol dehydrogenase isolated by its ability to complement an adhl mutation in S. cerevisiae; Sass et al., PNAS (USA), 83:9303 (1986)--S. cerevisiae PDE2 gene isolated by its ability to complement a RAS2.sup.va119 allele in S. cerevisiae strain TK161-R2V; Nikawa et al., Mol. Cell. Biol., 7:3629 (1987)--S. cerevisiae PDE1 gene isolated by transforming S. cerevisiae strain TK161-R2V; and Wilson, Molec. Cell. Biol., 8:505 (1988)--S. cerevisiae SRA5 gene isolated by virtue of its ability to rescue a RAS.sup.+ sra5-5 S. cerevisiae strain RW60-12C.
Yeast have also been used to isolate non-yeast genes. For example, Henikoff et al., Nature, 289:33 (1981), reported the isolation of a D. melanogaster gene by complementation of yeast mutants and Lee et al., Nature, 327:31 (1987), reported the isolation of human gene by its ability to complement a mutation in the cdc2 gene in S. pombe. The expression vector employed included a viral (SV40) promoter.
More recently, complementation screening has been used by the applicants herein to detect and isolate mammalian cDNA clones encoding certain types of phosphodiesterases (PDEs). Colicelli et al., PNAS (USA), 86:3599 (1989) reports the construction of a rat brain cDNA library in a Saccharomyces cerevisiae expression vector and the isolation therefrom of genes having the capacity to function in yeast to suppress the phenotypic effects of RAS2.sup.va119, a mutant form of, the RAS2 gene analogous to an oncogenic mutant of the human H-RAS gene. A rat species cDNA so cloned and designated DPD (dunce-like phosphodiesterase) has the capacity to complement the loss of growth control associated with an activated RAS2.sup.va119 gene harbored in yeast strains TK161-R2V. The gene encodes a high-affinity cAMP specific phosphodiesterase that is highly homologous to the cAMP phosphodiesterase encoded by the dunce locus of D. melanogaster.
Relatively few PDE genes have been cloned to date. Of those cloned, most belong to the cAMP-specific family of phosphodiesterases (cAMP-PDEs). See Davis, "Molecular Genetics of the Cyclic Nucleotide Phosphodiesterases", pp. 227-241 in Cyclic Nucleotide Phosphodiesterases: Structure, Regulation, and Drug Action, Beavo, J. and Houslay, M. D., Eds.; John Wiley & Sons, New York; 1990. See also, e.g., Faure et al., PNAS (USA), 85:8076 (1988)--D. discoideum; Sass et al., supra--S. cerevisiae, PDE class IV, designated PDE2; Nikawa et al., supra--S. cerevisiae. designated PDE1; Wilson et al., supra--S. cerevisiae, designated SRA5; Chen et al., PNAS (USA), 83:9313 (1986)--D. melanogaster, designated dnc.sup.+ ; Ovchinnikov, et al., supra--bovine retina, designated cGMP PDE; Davis et al., supra--rat liver, designated rat dnc-1; Colicelli, et al., supra--rat brain, designated DPD; Swinnen, et al., PNAS (USA), 86:5325 (1989)--rat testis, rat PDE1, PDE2, PDE3 and PDE4; and Livi, et al., Mol. Cell. Biol., 10:2678 (1990)--human monocyte, designated hPDE1. See also, LeTrong et al., Biochemistry, 29:10280 (1990) reporting cloning of a DNA encoding a fragment of a bovine adrenal cGMP stimulated PDE and Thompson et al., J. FASEB, 5(6):A1592 (Abstract No. 7092, 1991) reporting the cloning of a "Type II PDE" from rat pheochromocytoma cells.
Thus, there continues to exist a need in the art for improved cloning procedures effective for isolating genes, both of known and unknown function, for expression products sufficiently kinetically pure so as to be suitable for use in drug testing, and for drug screening methods that do not require kinetically pure protein preparations, and for the production of expression products having improved immunological specificity.